The SPECTRa Project :
A wider chemistry picture
Alan Tonge & Jim Downing
A Digital Repository for the Chemical Community
Project Overview
• 18-month project between University of Cambridge
and Imperial College London to develop customized
tools to deposit chemistry data in digital repositories
• Part of the JISC Digital Repositories programme
• Closely integrated with eBank and eCrystals (Bath and
Soton)
Requirements determined by survey
Requirements in a number of different user disciplines
•
synthetic organic chemistry
•
departmental crystallography services
•
computational chemistry
determined by interview and survey
The Problem
Science depends upon data
Experimental chemistry data is a resource / asset …
• Proprietary spectra formats (NMR, IR, UV) :
5-year shelf life
• PDF image files (supplementary data) :
not machine readable
• CIF xray :
90% remain unpublished
…most of which is lost or becomes unreadable
John Davies has 3000 unpublished
structures.
3000 x £300 cost per structure ~= £1M
Most of the problems are social,
not technical
The Solution
Capture selected data from chemistry workflows in open format
(JCAMP, MOL, CIF)
Add context-specific metadata +
Persistent identifiers
Deposit in Digital Repository
New feature (Controlled) public release
Internet
User search tools
OAI-PMH Metadata
Harvesting
Computational
Chemistry Calculations
NMR
Spectra
2D Chemical
Structures
SPECTRa Deposit Tools
Create CML, InChI, metadata
InChI :
InChI=1/C8H8O/c1-7(9)8-5-3-2-4-6-8/h2-6H,1H3
DSpace
Open
CML :
<molecule xmlns=“http://www.xml.cml.org/schema">
<atomArray>
<atom id="a1" elementType="C" x2="-0.380600" y2="-0.720800"/>
<atom id="a2" elementType="C" x2="-0.381800" y2="-1.548200"/>
<atom id="a3" elementType="C" x2="0.333100" y2="-1.961000"/>
<atom id="a4" elementType="C" x2="1.049500" y2="-1.547700"/>
<atom id="a5" elementType="C" x2="1.046600" y2="-0.717200"/>
<atom id="a6" elementType="C" x2="0.331300" y2="-0.308000"/>
<atom id="a7" elementType="C" x2="1.759600" y2="-0.302000"/>
<atom id="a8" elementType="C" x2="2.475600" y2="-0.711800"/>
<atom id="a9" elementType="O" x2="1.756400" y2="0.523000"/>
</atomArray>
<bondArray>
<bond atomRefs2="a4 a5" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a5 a6" order="2"/>
<bond atomRefs2="a6 a1" order="1"/>
<bond atomRefs2="a1 a2" order="2"/>
<bond atomRefs2="a5 a7" order="1"/>
<bond atomRefs2="a3 a4" order="2"/>
<bond atomRefs2="a7 a8" order="1"/>
<bond atomRefs2="a7 a9" order="2"/>
</bondArray>
</molecule>
SPECTRa Search Tools
OAI-PMH Harvesting
DSpace
Escrow
3D X-ray
Structures
Acknowledgements
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Project Director:
Chemistry leads:
Project Officers:
Project Manager:
Library Liaison:
Peter Morgan UL Cambridge
Henry Rzepa, Peter Murray-Rust
Fiona Cotterill, Jim Downing
Alan Tonge
Janet Evans, Lorraine Windsor
http://www.lib.cam.ac.uk/spectra/